hashCode() added for all the classes where added an equals()

valasatava · valasatava · commit 2d9003884da8 · 2017-03-28T11:47:23.000-07:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/alignment/SimpleAlignedSequence.java
@@ -270,37 +270,28 @@ public List<C> getAsList() {
 		return compounds;
 	}
 
-
+	@Override
 	public boolean equals(Object o){
 
 		if(! Equals.classEqual(this, o)) {
 			return false;
 		}
 
 		Sequence<C> other = (Sequence<C>)o;
-
 		if ( original.getAsList().size() != other.getAsList().size())
 			return false;
 
 		for ( int i = 0 ; i< original.getAsList().size() ; i++){
 			if ( ! original.getAsList().get(i).equalsIgnoreCase(other.getAsList().get(i)))
 				return false;
 		}
-
 		return true;
 	}
 
 	@Override
-	public boolean equals(Sequence<C>other){
-		if ( original.getAsList().size() != other.getAsList().size())
-			return false;
-
-		for ( int i = 0 ; i< original.getAsList().size() ; i++){
-			if ( ! original.getAsList().get(i).equalsIgnoreCase(other.getAsList().get(i)))
-				return false;
-		}
-
-		return true;
+	public int hashCode(){
+		String s = getSequenceAsString();
+		return s.hashCode();
 	}
 
 	@Override
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/SequenceFileProxyLoader.java
@@ -227,12 +227,9 @@ public boolean equals(Object o) {
 		}
 
 		Sequence<C> other = (Sequence<C>)o;
-
-
 		if ( other.getCompoundSet() != getCompoundSet())
 			return false;
 
-
 		List<C> rawCompounds = getAsList();
 		List<C> otherCompounds = other.getAsList();
 
@@ -245,9 +242,13 @@ public boolean equals(Object o) {
 			if ( ! myCompound.equalsIgnoreCase(otherCompound))
 				return false;
 		}
-
 		return true;
+	}
 
+	@Override
+	public int hashCode(){
+		String s = getSequenceAsString();
+		return s.hashCode();
 	}
 
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/StringProxySequenceReader.java
@@ -162,19 +162,17 @@ public SequenceView<C> getInverse() {
 		return SequenceMixin.inverse(this);
 	}
 
-
+	@Override
 	public boolean equals(Object o){
 
 		if(! Equals.classEqual(this, o)) {
 			return false;
 		}
 
 		Sequence<C> other = (Sequence<C>)o;
-
 		if ( other.getCompoundSet() != getCompoundSet())
 			return false;
 
-
 		List<C> rawCompounds = getAsList();
 		List<C> otherCompounds = other.getAsList();
 
@@ -187,9 +185,12 @@ public boolean equals(Object o){
 			if ( ! myCompound.equalsIgnoreCase(otherCompound))
 				return false;
 		}
-
 		return true;
+	}
 
-
+	@Override
+	public int hashCode(){
+		String s = getSequenceAsString();
+		return s.hashCode();
 	}
 }
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/loader/UniprotProxySequenceReader.java
@@ -257,6 +257,12 @@ public boolean equals(Object o){
 		return true;
 	}
 
+	@Override
+	public int hashCode(){
+		String s = getSequenceAsString();
+		return s.hashCode();
+	}
+
 	/**
 	 *
 	 * @return
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/storage/JoiningSequenceReader.java
@@ -300,43 +300,16 @@ public List<C> getAsList() {
 	}
 
 	@Override
-	public boolean equals(Sequence<C> other) {
-
-		if ( other.getCompoundSet() != getCompoundSet())
-			return false;
-
-
-		List<C> rawCompounds = getAsList();
-		List<C> otherCompounds = other.getAsList();
-
-		if ( rawCompounds.size() != otherCompounds.size())
-			return false;
-
-		for (int i = 0 ; i < rawCompounds.size() ; i++){
-			Compound myCompound = rawCompounds.get(i);
-			Compound otherCompound = otherCompounds.get(i);
-			if ( ! myCompound.equalsIgnoreCase(otherCompound))
-				return false;
-		}
-
-		return true;
-	}
-
-
-	public boolean equals(Sequence<C> o) {
-
+	public boolean equals(Object o) {
 
 		if(! Equals.classEqual(this, o)) {
 			return false;
 		}
 
 		Sequence<C> other = (Sequence<C>)o;
-
-
 		if ( other.getCompoundSet() != getCompoundSet())
 			return false;
 
-
 		List<C> rawCompounds = getAsList();
 		List<C> otherCompounds = other.getAsList();
 
@@ -349,10 +322,14 @@ public boolean equals(Sequence<C> o) {
 			if ( ! myCompound.equalsIgnoreCase(otherCompound))
 				return false;
 		}
-
 		return true;
 	}
 
+	@Override
+	public int hashCode(){
+		String s = getSequenceAsString();
+		return s.hashCode();
+	}
 
 	@Override
 	public int getIndexOf(C compound) {
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractSequence.java
@@ -520,6 +520,7 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {
 		this.compoundSet = compoundSet;
 	}
 
+	@Override
 	public boolean equals(Object o){
 
 		if(! Equals.classEqual(this, o)) {
@@ -547,6 +548,7 @@ public boolean equals(Object o){
 		return true;
 	}
 
+	@Override
 	public int hashCode(){
 		String s = getSequenceAsString();
 		return s.hashCode();
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Sequence.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/Sequence.java
@@ -79,10 +79,6 @@ public interface Sequence<C extends Compound> extends Iterable<C>, Accessioned {
 	 */
 	public List<C> getAsList();
 
-	public boolean equals(Sequence<C> other);
-
-	public int hashCode();
-
 	/**
 	 * Returns a portion of the sequence from the different positions. This is
 	 * indexed from 1
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/SequenceProxyView.java
@@ -72,7 +72,7 @@ public List<C> getAsList() {
 		return SequenceMixin.toList(this);
 	}
 
-
+	@Override
 	public boolean equals(Object o) {
 
 		if(! Equals.classEqual(this, o)) {
@@ -81,13 +81,13 @@ public boolean equals(Object o) {
 
 		Sequence<C> other = (Sequence<C>)o;
 
-
 		return sequence.equals(other);
 	}
 
 	@Override
-	public boolean equals(Sequence<C> other) {
-		return sequence.equals(other);
+	public int hashCode(){
+		String s = getSequenceAsString();
+		return s.hashCode();
 	}
 
 	@Override

Original file line number	Diff line number	Diff line change
`@@ -162,19 +162,17 @@ public SequenceView<C> getInverse() {`
`162`	`162`	`return SequenceMixin.inverse(this);`
`163`	`163`	`}`
`164`	`164`
`165`		`-`
	`165`	`+ @Override`
`166`	`166`	`public boolean equals(Object o){`
`167`	`167`
`168`	`168`	`if(! Equals.classEqual(this, o)) {`
`169`	`169`	`return false;`
`170`	`170`	`}`
`171`	`171`
`172`	`172`	`Sequence<C> other = (Sequence<C>)o;`
`173`		`-`
`174`	`173`	`if ( other.getCompoundSet() != getCompoundSet())`
`175`	`174`	`return false;`
`176`	`175`
`177`		`-`
`178`	`176`	`List<C> rawCompounds = getAsList();`
`179`	`177`	`List<C> otherCompounds = other.getAsList();`
`180`	`178`
`@@ -187,9 +185,12 @@ public boolean equals(Object o){`
`187`	`185`	`if ( ! myCompound.equalsIgnoreCase(otherCompound))`
`188`	`186`	`return false;`
`189`	`187`	`}`
`190`		`-`
`191`	`188`	`return true;`
	`189`	`+ }`
`192`	`190`
`193`		`-`
	`191`	`+ @Override`
	`192`	`+ public int hashCode(){`
	`193`	`+ String s = getSequenceAsString();`
	`194`	`+ return s.hashCode();`
`194`	`195`	`}`
`195`	`196`	`}`
Original file line number	Diff line number	Diff line change
`@@ -257,6 +257,12 @@ public boolean equals(Object o){`
`257`	`257`	`return true;`
`258`	`258`	`}`
`259`	`259`
	`260`	`+ @Override`
	`261`	`+ public int hashCode(){`
	`262`	`+ String s = getSequenceAsString();`
	`263`	`+ return s.hashCode();`
	`264`	`+ }`
	`265`	`+`
`260`	`266`	`/**`
`261`	`267`	`*`
`262`	`268`	`* @return`
Original file line number	Diff line number	Diff line change
`@@ -520,6 +520,7 @@ public void setCompoundSet(CompoundSet<C> compoundSet) {`
`520`	`520`	`this.compoundSet = compoundSet;`
`521`	`521`	`}`
`522`	`522`
	`523`	`+ @Override`
`523`	`524`	`public boolean equals(Object o){`
`524`	`525`
`525`	`526`	`if(! Equals.classEqual(this, o)) {`
`@@ -547,6 +548,7 @@ public boolean equals(Object o){`
`547`	`548`	`return true;`
`548`	`549`	`}`
`549`	`550`
	`551`	`+ @Override`
`550`	`552`	`public int hashCode(){`
`551`	`553`	`String s = getSequenceAsString();`
`552`	`554`	`return s.hashCode();`
Original file line number	Diff line number	Diff line change
`@@ -72,7 +72,7 @@ public List<C> getAsList() {`
`72`	`72`	`return SequenceMixin.toList(this);`
`73`	`73`	`}`
`74`	`74`
`75`		`-`
	`75`	`+ @Override`
`76`	`76`	`public boolean equals(Object o) {`
`77`	`77`
`78`	`78`	`if(! Equals.classEqual(this, o)) {`
`@@ -81,13 +81,13 @@ public boolean equals(Object o) {`
`81`	`81`
`82`	`82`	`Sequence<C> other = (Sequence<C>)o;`
`83`	`83`
`84`		`-`
`85`	`84`	`return sequence.equals(other);`
`86`	`85`	`}`
`87`	`86`
`88`	`87`	`@Override`
`89`		`- public boolean equals(Sequence<C> other) {`
`90`		`- return sequence.equals(other);`
	`88`	`+ public int hashCode(){`
	`89`	`+ String s = getSequenceAsString();`
	`90`	`+ return s.hashCode();`
`91`	`91`	`}`
`92`	`92`
`93`	`93`	`@Override`